Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

[摘要] BackgroundStructured non-coding RNAs play many different roles in the cells, but the annotation of these RNAs is lacking even within the human genome. The currently available computational tools are either too computationally heavy for use in full genomic screens or rely on pre-aligned sequences.MethodsHere we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes without alignment.ResultsOur computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity.ConclusionsDotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs.

[发布日期] 2017-12-02

[关键词] Non-coding RNA;Secondary structure;Gene finding